Skill trees generally makes game a worse, and ruin the experience, and so do stat investments. It's not something very obvious, it FEELS fun. Seeing a massive skill tree can feel like an ocean of possibilities and experimentation, but in nearly every case, it's the exact opposite. Skill trees almost always massively reduce the amount of the game your actually playing, and remove most excitement from a game.
Weapon Requirement skill tree games
Nioh, Etrian Odyssey, and Dragon quest 8 are examples i will categorize into "Weapon Requirement skill tree games". The moment you acquire a skill giving 10% damage bonus to swords, other weapon types are instantly killed. No longer are you even excited to find a good axe, when the weakness of swords is not mitigated and their speedy identity like better frame data or faster turn order make them far better options. It doesn't just unfairly tip the scales, it heavily kills all interest in every other weapon in the game. Plus, the moment you get more then 1 weapon requirement skill, even at just two of these, you'll be using swords the rest of the game, and now
Worse yet, the moment skills like flame slash appear, your never touching those other weapons for sure. Investing in knifes or whips on your nightseeker in Etrian IV, is a decision of no return. You will never touch the other weapon type again. Similarly, investing in rods on your healer in DQ8, probably means your never touching boomerangs the entire game. You no longer care for 96% of all weapons in the game, as even for your weapon type, you'll probably only change to a better one 4-5 times the entire game. As you continue finding more and more equipment you "can't", or rather won't use around every corner, it inevitably affects you, that your just not having as much fun as you could be, would the game let you experiment more. In Nioh, investing in spears probably means not looking at swords or sickles. And for an action game where all the weapons have the exact same attack animations and no active skills outside of weapons, this significantly harms gameplay variety. Just pick a weapon, and use it's attack animations, and only it's animations, for the next 100+ hours. Want to change weapons? to fucking bad, you will lose every skill you have ever learned. It's just not fun.
Requirement based skill trees (Branching trees)
Final Fantasy 10, and SMT Digital Devil Saga, are all games that are "Requirement based". One might think simply by removing the "Weapon" part, the problem would be solved, but it's not. Although no longer requiring a weapon, later games skills still generally require heavily investing points towards something, and usually requiring so many fucking points you basically have to give up experiencing a huge amount of the rest of the entire game to do so. In FFX, if you want yuna to use black magic, outside of using a very limited teleport sphere, you have to invest probably around 50 levels of skill points just to get to the START of the black magic tree. Now, while FFX is kind of a ultra cherry picked example as it's probably the worst skill tree in all of gaming that doesn't have weapon requirements, Digital Devil Saga does the exact same thing. If your in mid game but want the protagonist to learn tier 3 thunder magic, you've basically decided that literally the rest of the entire game is already surrendered. You will never, learn or use literally anything else the entire game, because of how ridiculously high the cost is to learn a full tree like that. In basically every game using tree line skill trees, there is always an EXTREME opportunity cost associated with the skill tree.
Final Fantasy 13, a game where it's basically the most tame it can get, the skill tree still detracts from the game. Despite what the investment screen looks like in this game, you are effectively investing points in a class. Depending on how many points are invested, you can spend some to get optional extras. The problem here still, it's basically dragon quest 8 all over again. Your abilities may not be weapon locked, but their class locked, and it's effectively the same. It IS a better system, as you can enjoy every weapon you find. But it still kills experimentation, your still locked into your specialization. While unlike DQ8 they made you get increasingly more points to invest as the game goes on so you can easily acquire early game stuff for a different class, why the fuck would you? Why would i invest this character as a medic, when i can just keep them focused on being a mage, and make another character a medic. Both characters WILL perform better when specialized, they will get access to higher tier stuff far sooner, and because you can't get that if you experiments, your punished for trying out what your characters can do. The game much like DQ8 also has less then 10 active skills / spells per class, so your mostly using the exact same stuff the entire game. The nail in the coffin, is each character actually has unique endgame abilities in every class. Sazh will learn different spells then Hope, but with 6 classes, 6 characters, and the player being REQUIRED (the theme of this section) to invest such an extreme amount of points to get so far in another class "tree", it's substantially best not to. Everyone should pick a main class and fully invest in it, and doing anything else massively lowers your endgame power.
Discouraging Skill Trees, Stat Investments, & Skill Grids
Games are often great, when the player can freely invest points without needing other investments first, when doing so is either discouraged from going to far, or outright actively prevented from doing so.
Dark souls 1 will be my first example (altho all dark souls games apply). In these games, weapons have stat requirements rather then infinitely scaling with investment. Going even further, the games puts soft and hard caps on stats. Yet, even hitting the soft caps are strongly discouraged, weapons scale almost not at all from stat points, and stat points are better off spend hitting requirements to equip a weapon at all. This lets players specialize, without actually encouraging them to do so, and goes father to actively discourage them. Many STR weapons even have slight DEX requirements, the stat that decides casting speed for spells, that themself are also stat requirement based, rather then scaling well. Everything in dark souls pushes the player to invest around in different stats, and effectively punishes you for specializing, as you get far less in return, then if you invested like a red mage and had a mix of magical and physical. Notice how the dark souls series is still on the very top of popularity charts?
Final Fantasy 12 is a game with a giant skill grid, but despite allowing the player complete freedom to invest towards anything from the very start, it puts a huge emphasis on both player experimentation, and preventing hyper specialization. In this game, the nodes on the skill grid are merely "licenses", permission to use a weapon, or a skill, and usually come in packs. For example, a node can give like license for 5 different spears. With that license purchased, if you own those spears, you can equip them. If you don't own them yet, having not found them in game or not yet purchased them from a shop, then getting the license pack actually doesn't do anything. The same applies to skills, spells, and so on. Getting the license for the revive spell won't matter if you didn't find the spell ingame yet. Stat nodes do exist on the grid, but are less common. This system does more then just allowing you to skip early game equips and skills and instead get stats, it allows you to use swords like 50% of the game, find a really good looking axe, and purchase the axe license immediately. There are also NO weapon specific skills. Anyone can use any skill with any weapon, and you can freely and instantly use a mid or even late game weapon type you haven't used the entire game, just as well as another player who used nothing but that weapon type the entire game. The games strong emphasis not not allowing players to actually specialize, creates a system where players can both freely experiment, and actually check out every single new weapon they find. Even more, skills cost LP (License points), something earned from every battle, they aren't limited to level up rewards, and the game can even be beaten without ever leveling up. These systems give this game much more staying power, and why it keeps getting remasters and new editions.
Dragon Quest 11S is a unusual case. There are weapon based skills, but the skill tree is both only about 80 nodes, and far more importantly, the player can respec at anytime. There is a respec cost, but on the hardest difficulty (a full draconian run) the player has tons of money they simply can't run out of in normal gameplay, and can burn it all constantly changing their build for literally every single fight if they wanted to. Ontop of this, much like FF12, it's a skill grid and not line based. That is to say, you only need to learn any adjacent skill node, then learn the one you want. You can respec and skip early game skills, and even learn a whip skill on a way to a boomerang skill, simply because it takes less nodes to get to the goal. Most of all, emphasis again on freely respeccing at any time. If you find a new weapon you like, equip it and swap your skill tree around. This approach allows you to be interested in every single weapon you find despite the weapon requirements, and the players ability to freely experiment is again why this game was such a smash hit that it got release after release, with new version after new version after new version, with constant expansions. it's really fun!
Tales of Xillia, is an unusual mix. It's another skill grid type game, and without weapon type requirements. However, the further away you are from the start of the grid, the bigger the stat bonuses are, and the better the skills are. More then just discouraging specialization, it substantially kills it off. When the game starts, the grid is a decent size, but can be expanded. To expand the skill grid, you have to acquire a specific skill on the outter ring of the skill grid called the key skill, and any 2 other skills on the outer ring. The game is designed such that, one layer of the ring, the key is in the top left, and next time it's in the very bottom right. You won't know where it will appear, but the game does a good job of effectively forcing you to invest skill points all over the entire grid. Moreover, you can pick how you get there. You could get to the bottom right straight through the middle, or go around the northeast edge, or from the southwest edge, etc. The general strategy is just, keep expensing it as many times as possible, all the best skills are going to be unlocked last. But also, if you come across a boss you really need a water element arte/skill for, you can at anytime just look at the stuff you skipped over already, and grab something. It makes hyper specializing "simple", by saying that every characters at their best if you just expand the skill grid as much as possible. There aren't other better options, it's intended to be obviously the best decision at every moment, unless you get stuck, or your having problems with specific enemys. It fixes the "specialization" and requirement problems, by baking in a requirement (to expand the skill grid) and specialization (to again, expand the skill grid) into the core of it. Your never limited out of weapon types because there are no weapon types, and any active skills or spells your interested in, just grab. After all, you had to learn stuff all over the grid to get these keys to expand the grid anyway, your never more then 2-3 nodes away from touching any skill on the entire grid. Also, were getting a tales of xillia remaster.
Conclusions, and Tree-less skill systems
Basically, skill trees in their most common form, ones where you need to learn X, to learn Y, to learn Z, in a series / "tree", aren't just less popular, their also bad. They actively hinder their players from experiencing as much of the game as they otherwise could if those systems weren't implemented.
I don't like skill trees very much. Sometimes their exciting like the above named games, but mostly their just bad. Instead, consider a "Tree-less" system. Games like Paper mario, or Tales of Vesperia, where you have to find skills, or find weapons and learn them from then, and then finally equip a limited amount of your skills using some type of skill points. The Kingdom hearts series also does this exact same thing, at first it only has equip skills, but later adds elements of finding skills in chests or as rewards from optional quests or bosses. Additionally, deciding what skills to equip, increases the complexity of the strategy layer of a game. Changing your setup for a boss fight is fun! Look at games like Persona 3/4/5 (and all SMT games), and their VERY strong encouragement of changing your setup rather then grinding or investing skill points. In fact, the EXP system in SMT games is very interesting. Every creature usually only gets like 3-5 skills as it levels up, but those are more then anything meant to make it feel "RPG-like" and "Level-up decision making", without actually mattering almost at all. Not only do you generally just fuse your creature away into a new one losing basically all your previous skills, but even if you wanted to grind a creature up, the EXP system applies a massive X% penalty for each level a creature is over it's recruitment level. This is meant to make it strongly unreasonable to just keep investing EXP into one creature (kind of like the topic of investing skill points or stat points, and how all those other best games discourage it to!) and strongly pressures the player to stop doing so and change things up.
The next time you see a giant, requirement based skill tree, especially if weapon types are involved.... consider how much more fun another, different game would be, that didn't lock your playstyle the entire game into whatever specialization you decide at the start. The weapons, armor, and skills you'd be able to play with. It matters. Investment systems that don't heavily restrict or completely ban specialization, kill player enjoyment, and we deserve better games.